1S26

Structure of Anthrax Edema Factor-Calmodulin-alpha,beta-methyleneadenosine 5'-triphosphate Complex Reveals an Alternative Mode of ATP Binding to the Catalytic Site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.264 
  • R-Value Observed: 0.264 

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This is version 1.4 of the entry. See complete history


Literature

Structure of anthrax edema factor-calmodulin-adenosine-5'-(alpha,beta-methylene)-triphosphate complex reveals an alternative mode of ATP binding to the catalytic site

Shen, Y.Guo, Q.Zhukovskaya, N.L.Drum, C.L.Bohm, A.Tang, W.-J.

(2004) Biochem Biophys Res Commun 317: 309-314

  • DOI: https://doi.org/10.1016/j.bbrc.2004.03.046
  • Primary Citation of Related Structures:  
    1S26

  • PubMed Abstract: 

    Anthrax edema factor (EF) is a key virulence factor secreted by Bacillus anthracis. Here, we report a structure, at 3.0 A resolution, of the catalytic domain of EF (EF3) in complex with calmodulin (CaM) and adenosine 5'-(alpha,beta-methylene)-triphosphate (AMPCPP). Although the binding of the triphosphate of AMPCPP to EF3 can be superimposed on that of previously determined 3'deoxy-ATP (3'dATP) and 2'deoxy 3' anthraniloyl-ATP (2'd3' ANT-ATP) in EF3-CaM, the ribose and the adenine rings of AMPCPP are rotated approximately 105 and 180 degrees, respectively, relative to those of 3'dATP and 2'd3'ANT-ATP. Based on this model, K382 and F586 should play key roles in the recognition of adenine. However, mutations of these residues to alanine either separately or together cause only modest changes in Michaelis-Menten constants and IC50 values of AMPCPP and cAMP. Therefore, this alternate binding mode of the adenosine of AMPCPP binds to EF likely playing only a minor role in ATP binding and in catalysis.


  • Organizational Affiliation

    Ben-May Institute for Cancer Research, The University of Chicago, 924 East 57th Street, Chicago, IL 60637, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Calmodulin-sensitive adenylate cyclase
A, B, C
510Bacillus anthracisMutation(s): 0 
Gene Names: CYAPXO1-122
EC: 4.6.1.1
UniProt
Find proteins for P40136 (Bacillus anthracis)
Explore P40136 
Go to UniProtKB:  P40136
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40136
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Calmodulin
D, E, F
148Homo sapiensMutation(s): 0 
Gene Names: CALM1CAM1CALMCAMCALM2CAM2CAMBCALM3CAM3CAMC
UniProt & NIH Common Fund Data Resources
Find proteins for P0DP23 (Homo sapiens)
Explore P0DP23 
Go to UniProtKB:  P0DP23
PHAROS:  P0DP23
GTEx:  ENSG00000198668 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DP23
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
APC
Query on APC

Download Ideal Coordinates CCD File 
H [auth A],
J [auth B],
L [auth C]
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
C11 H18 N5 O12 P3
CAWZRIXWFRFUQB-IOSLPCCCSA-N
YB
Query on YB

Download Ideal Coordinates CCD File 
G [auth A],
I [auth B],
K [auth C]
YTTERBIUM (III) ION
Yb
AWSFICBXMUKWSK-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
M [auth D]
N [auth D]
O [auth E]
P [auth E]
Q [auth F]
M [auth D],
N [auth D],
O [auth E],
P [auth E],
Q [auth F],
R [auth F]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
APC PDBBind:  1S26 Ki: 8.50e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.264 
  • R-Value Observed: 0.264 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.555α = 90
b = 167.605β = 90
c = 345.346γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-04-13
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-11-20
    Changes: Advisory, Derived calculations
  • Version 1.4: 2024-02-14
    Changes: Advisory, Data collection, Database references, Derived calculations